In this study sprouting two different wheat cultivars under various environmental conditions revealed that varietal variation is the most important factor affecting α-amylase quantity as well as quality to modify flour functionality significantly, followed by pre-soaking duration and temperature. Sprouted wheat flour post five days germination was utilized at different rates to prepare 100 g composite breads. There was an improvement in baking quality and shelf life of breads containing 1% and 5% sprouted flour resulting in a significantly increased loaf volume, better texture, and less retrogradation during 7 days post baking than the control. This study presents opportunities for industry to fortify baked products with sprouted wheat flour to yield functional whole grain products that are nutrient dense and naturally shelf-stable.